2BEO | pdb_00002beo

PrfA, Transcriptional Regulator In Listeria Monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OMI	PDB ENTRY 1OMI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		20 % (W/V) PEG 6000 100 MM NA-MES PH6.5 1 M LICL, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.951	α = 90
b = 80.713	β = 111.91
c = 60.965	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	RH-COATED SILICON MIRROR	2003-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	30	89	0.01	10.6	1.76		12402		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	68.9		0.03	3.1	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OMI	2.7	56.8	11790	602	91.9	0.246	0.244	0.24	0.289	0.3	RANDOM	22.92

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
4.66		8.23	-2.29		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.823
r_dihedral_angle_3_deg	17.854
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_1_deg	5.433
r_scangle_it	3.616
r_mcangle_it	3.224
r_scbond_it	2.501
r_mcbond_it	2.288
r_angle_refined_deg	1.944
r_angle_other_deg	1.382
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.193
r_symmetry_vdw_other	0.183
r_nbtor_refined	0.176
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.145
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.006
r_bond_other_d	0.004
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3740
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing